- Align the orthologous sequences with MUSCLE [32](see
Note 12) and store the alignment in the appropriate file for-
mat. Most tree reconstruction software accept the FASTA and
Phylip formats as input (Fig.9;seeNotes 13and 14 ). For file
format conversion at a later step in the analysis, you can use
online tools such as ALTER [38], the format converter avail-
able athttp://phylogeny.lirmm.fr/phylo_cgi/data_converter.
cgi, or the sequence alignment tool ClustalW [39] with the
option–reformat.
Fig. 8Mapping identified orthologs on the reference pathway. Tracing representation of human AMPK
pathway components inMus musculus,Drosophila melanogaster,Saccharomyces cerevisiae,Arabidopsis
thaliana,Methanocaldococcus jannaschii(archaea), andChloroflexus aurantiacus(bacteria). Each protein is
represented as a box, and every box is divided into six columns, and each column represents the presence/
absence of the protein in corresponding species. If an ortholog to a pathway component is represented in a
species, the corresponding column is colored. The columns represent from left to right the order of the species
list above
Tracing AMPK Evolution 131